A silica gel-modified borage biochar (BB@Si) was first produced and used as a binding agent for potentially hazardous Ni2+ ions in aqueous systems. The recommended biochar was more effective in eliminating Ni2+ than pristine biochar (BB). Its maximum qm could reach up to 1.39 × 10−3 mol/g at 30 °C, and sorption isotherms showed that the Langmuir model could more accurately define its sorption behavior. The Dubinin-Radushkevich isotherm also revealed that the average sorption energy ranged from 11.00 to 11.14 kJ/mol. Zeta potential tests, SEM images, and FT-IR scans confirmed the interactions between BB@Si and Ni2+ ions. Dynamic flow treatment studies showed high uptake effectiveness when the flow rate and amount of BB@Si were suitable. Nickel desorption yield of around 80% from BB@Si was noted with 0.01 M HCl. The BB@Si column's breakthrough and exhausted points were identified to be 45 and 352 min, respectively. Its maximum exhaustion capacity value was determined to be 52.73 mg/g. Ni2+ removal from the actual wastewater sample exceeded 75%. The resulting outcomes imply the immense potential of employing BB@Si in the treatment of Ni2+– contaminated aqueous systems.